def establish_processor(self, loop_counter=0):
if loop_counter == 0 and self.master_equation_flag == False:
new_file, original_rxn_eqs, master_rxn_eqs = ctic.cti_write2(
original_cti=os.path.join(self.data_directory,
self.cti_file_name),
working_directory=self.data_directory,
file_name=self.cti_file_name.replace('.cti', '') + '_updated')
self.new_cti_file = new_file
if loop_counter == 0 and self.master_equation_flag == True:
new_file, original_rxn_eqs, master_rxn_eqs = ctic.cti_write2(
original_cti=os.path.join(self.data_directory,
self.cti_file_name),
master_rxns=os.path.join(
self.data_directory,
self.master_reaction_equation_cti_name),
master_index=self.master_index,
working_directory=self.data_directory,
file_name=self.cti_file_name.replace('.cti', '') + '_updated')
self.new_cti_file = new_file
processor = pr.Processor(self.new_cti_file)
#processor = pr.Processor(self.data_directory +'/'+ self.cti_file_name)
self.processor = processor
return
def updating_files(self, loop_counter=0):
if loop_counter == 0:
updated_file_name_list = self.yaml_instance.yaml_file_updates(
self.yaml_file_list_with_working_directory,
self.list_of_parsed_yamls,
self.experiment_dictonaries,
self.physical_obervable_updates_list,
loop_counter=loop_counter)
self.updated_file_name_list = updated_file_name_list
updated_absorption_file_name_list = self.yaml_instance.absorption_file_updates(
self.updated_file_name_list,
self.list_of_parsed_yamls,
self.experiment_dictonaries,
self.absorbance_coef_update_dict,
loop_counter=loop_counter)
else:
updated_file_name_list = self.yaml_instance.yaml_file_updates(
self.updated_yaml_file_name_list,
self.list_of_parsed_yamls,
self.experiment_dictonaries,
self.physical_obervable_updates_list,
loop_counter=loop_counter)
updated_absorption_file_name_list = self.yaml_instance.absorption_file_updates(
self.updated_yaml_file_name_list,
self.list_of_parsed_yamls,
self.experiment_dictonaries,
self.absorbance_coef_update_dict,
loop_counter=loop_counter)
#print(self.original_experimental_conditions_local[0]['coupledCoefficients'],' ',loop_counter,'post simulation')
self.updated_absorption_file_name_list = updated_absorption_file_name_list
self.updated_yaml_file_name_list = self.updated_absorption_file_name_list
if self.master_equation_flag == True and loop_counter / 1 == loop_counter:
master_equation_surrogate_model_update_dictonary = self.master_equation_instance.surrogate_model_molecular_parameters_chevy(
self.sensitivity_dict, self.master_equation_reactions,
self.delta_x_molecular_params_by_reaction_dict)
self.master_equation_surrogate_model_update_dictonary = master_equation_surrogate_model_update_dictonary
#this may not be the best way to do this
if self.master_equation_flag == True and loop_counter / 1 != loop_counter:
master_equation_surrogate_model_update_dictonary = self.master_equation_instance.surrogate_model_molecular_parameters_chevy(
self.sensitivity_dict, self.master_equation_reactions,
self.delta_x_molecular_params_by_reaction_dict)
self.master_equation_surrogate_model_update_dictonary = master_equation_surrogate_model_update_dictonary
if self.master_equation_flag == False:
self.master_equation_surrogate_model_update_dictonary = {}
#update the cti files pass in the renamed file
# is this how this function works
if self.master_equation_flag == True:
new_file, original_rxn_eqs, master_rxn_eqs = ctic.cti_write2(
x=self.deltaXAsNsEas,
original_cti=self.data_directory + '/' + self.cti_file_name,
master_rxns=self.data_directory + '/' +
self.master_reaction_equation_cti_name,
master_index=self.master_index,
MP=self.master_equation_surrogate_model_update_dictonary,
working_directory=self.data_directory,
file_name=self.cti_file_name.replace('.cti', '') + '_updated')
if self.master_equation_flag == False:
new_file, original_rxn_eqs, master_rxn_eqs = ctic.cti_write2(
x=self.deltaXAsNsEas,
original_cti=self.data_directory + '/' + self.cti_file_name,
MP=self.master_equation_surrogate_model_update_dictonary,
working_directory=self.data_directory,
file_name=self.cti_file_name.replace('.cti', '') + '_updated')
self.new_cti_file = new_file
return
import sys
sys.path.append(
'.'
) #get rid of this at some point with central test script or when package is built
import MSI.simulations.instruments.shock_tube as st
import MSI.cti_core.cti_processor as pr
import MSI.optimization.matrix_loader as ml
import MSI.optimization.opt_runner as opt
import MSI.simulations.absorbance.curve_superimpose as csp
import MSI.simulations.yaml_parser as yp
import MSI.cti_core.cti_combine as ctic
import cantera as ct
ctiFile = 'MSI/data/test_data/FFCM1.cti'
test_p = pr.Processor('MSI/data/test_data/FFCM1.cti')
ctiFile_Name = 'FFCM1'
new_file, original_rxn_eqs, master_rxn_eqs = ctic.cti_write2(
original_cti=ctiFile,
working_directory='MSI/data/test_data',
file_name='FFCM1_updated_file')
